Remove legacy extended internal dependencies reports and notebooks

CHANGELOG.md

@@ -534,11 +534,11 @@ For all details see: https://github.com/JohT/code-graph-analysis-pipeline/releas
 ### 📖 Jupyter Notebook Reports
 
 * [External Dependencies](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/external-dependencies-java/ExternalDependenciesJava.md) contains detailed information about external library usage ([Notebook](./domains/external-dependencies/explore/ExternalDependenciesJava.ipynb)).
-* [Object Oriented Design Quality Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/object-oriented-design-metrics-java/ObjectOrientedDesignMetricsJava.md) is based on [OO Design Quality Metrics by Robert Martin](https://api.semanticscholar.org/CorpusID:18246616) ([Notebook](./jupyter/ObjectOrientedDesignMetricsJava.ipynb)).
+* [Object Oriented Design Quality Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/object-oriented-design-metrics-java/ObjectOrientedDesignMetricsJava.md) is based on [OO Design Quality Metrics by Robert Martin](https://api.semanticscholar.org/CorpusID:18246616) ([Notebook](./domains/internal-dependencies/explore/ObjectOrientedDesignMetricsJava.ipynb)).
 * [Overview](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/overview-java/OverviewJava.md) contains overall statistics and details about methods and their complexity. ([Notebook](./jupyter/OverviewJava.ipynb)).
 * [Internal Dependencies](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/internal-dependencies-java/InternalDependenciesJava.md) is based on [Analyze java package metrics in a graph database](https://joht.github.io/johtizen/data/2023/04/21/java-package-metrics-analysis.html) and also includes cyclic dependencies ([Notebook](./domains/internal-dependencies/explore/InternalDependenciesJava.ipynb)).
-* [Visibility Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/visibility-metrics-java/VisibilityMetricsJava.md) ([Notebook](./jupyter/VisibilityMetricsJava.ipynb)).
-* [Wordcloud](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/wordcloud/Wordcloud.md) contains a visual representation of package and class names ([Notebook](./jupyter/Wordcloud.ipynb)).
+* [Visibility Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/visibility-metrics-java/VisibilityMetricsJava.md) ([Notebook](./domains/internal-dependencies/explore/VisibilityMetricsJava.ipynb)).
+* [Wordcloud](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/wordcloud/Wordcloud.md) contains a visual representation of package and class names ([Notebook](./domains/internal-dependencies/explore/Wordcloud.ipynb)).
 
 ### 📖 Graph Data Science Reports
 
@@ -551,8 +551,8 @@ Here are some reports that utilize Neo4j's [Graph Data Science Library](https://
 ### 📖 Other Reports
 
 * [External Dependencies (CSV)](./domains/external-dependencies/externalDependenciesCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/external-dependencies-csv/External_package_usage_overall.csv))
-* [Object Oriented Design Metrics (CSV)](./scripts/reports/ObjectOrientedDesignMetricsCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/object-oriented-design-metrics-csv/MainSequenceAbstractnessInstabilityDistanceJava.csv))
 * [Overview (CSV)](./scripts/reports/OverviewCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/overview-csv/Cyclomatic_Method_Complexity.csv))
 * [Internal Dependencies - Cyclic (CSV)](./domains/internal-dependencies/internalDependenciesCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/internal-dependencies-csv/Cyclic_Dependencies_Breakdown_Backward_Only.csv))
 * [Internal Dependencies - Interface Segregation (CSV)](./domains/internal-dependencies/internalDependenciesCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/internal-dependencies-csv/InterfaceSegregationCandidates.csv))
-* [Visibility Metrics (CSV)](./scripts/reports/VisibilityMetricsCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/visibility-metrics-csv/RelativeVisibilityPerArtifact.csv))
+* [Object Oriented Design Metrics (CSV)](./domains/internal-dependencies/internalDependenciesCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/object-oriented-design-metrics-csv/MainSequenceAbstractnessInstabilityDistanceJava.csv))
+* [Visibility Metrics (CSV)](./domains/internal-dependencies/internalDependenciesCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/visibility-metrics-csv/RelativeVisibilityPerArtifact.csv))

COMMANDS.md

@@ -407,7 +407,7 @@ The script [executeJupyterNotebookReport.sh](./scripts/executeJupyterNotebookRep
 - data availability validation using [executeQueryFunctions.sh](#executequeryfunctionssh)
 - executing and converting the given Notebook using [executeJupyterNotebook.sh](#execute-a-notebook-with-executejupyternotebooksh)
 
-Here is an example on how to run the report [Wordcloud.ipynb](./jupyter/Wordcloud.ipynb):
+Here is an example on how to run the report [Wordcloud.ipynb](./domains/internal-dependencies/explore/Wordcloud.ipynb):
 
 ```shell
 ./scripts/executeJupyterNotebookReport.sh  --jupyterNotebook Wordcloud.ipynb
@@ -425,10 +425,10 @@ You can search the messages `Validation succeeded` or `Validation failed` inside
 
 [executeJupyterNotebook.sh](./scripts/executeJupyterNotebook.sh) executes a Jupyter Notebook in the command line and convert it to different formats like Markdown and PDF (optionally). It takes care of [setting up the environment](#manually-setup-the-environment-using-conda) and [uses nbconvert](#executing-jupyter-notebooks-with-nbconvert) to execute the notebook and convert it to other file formats under the hood.
 
-Here is an example on how to use [executeJupyterNotebook.sh](./scripts/executeJupyterNotebook.sh) to for example run [Wordcloud.ipynb](./jupyter/Wordcloud.ipynb):
+Here is an example on how to use [executeJupyterNotebook.sh](./scripts/executeJupyterNotebook.sh) to for example run [Wordcloud.ipynb](./domains/internal-dependencies/explore/Wordcloud.ipynb):
 
 ```shell
-./scripts/executeJupyterNotebook.sh ./jupyter/Wordcloud.ipynb
+./scripts/executeJupyterNotebook.sh ./domains/internal-dependencies/explore/Wordcloud.ipynb
 ```
 
 ### Manually setup the environment using Conda

README.md

@@ -51,10 +51,10 @@ Here is an overview of [Jupyter Notebooks](https://jupyter.org) reports from [co
 - [Internal Dependencies](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/internal-dependencies-java/InternalDependenciesJava.md) is based on [Analyze java package metrics in a graph database](https://joht.github.io/johtizen/data/2023/04/21/java-package-metrics-analysis.html) and also includes cyclic dependencies ([Notebook](./domains/internal-dependencies/explore/InternalDependenciesJava.ipynb)).
 - [Method Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/method-metrics-java/MethodMetricsJava.md)  shows how the effective number of lines of code and the cyclomatic complexity are distributed across the methods in the code ([Notebook](./jupyter/MethodMetricsJava.ipynb)).
 - [Node Embeddings](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/node-embeddings-java/NodeEmbeddingsJava.md) shows how to generate node embeddings and to further reduce their dimensionality to be able to visualize them in a 2D plot ([Notebook](./jupyter/NodeEmbeddingsJava.ipynb)).
-- [Object Oriented Design Quality Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/object-oriented-design-metrics-java/ObjectOrientedDesignMetricsJava.md) is based on [OO Design Quality Metrics by Robert Martin](https://api.semanticscholar.org/CorpusID:18246616) ([Notebook](./jupyter/ObjectOrientedDesignMetricsJava.ipynb)).
+- [Object Oriented Design Quality Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/object-oriented-design-metrics-java/ObjectOrientedDesignMetricsJava.md) is based on [OO Design Quality Metrics by Robert Martin](https://api.semanticscholar.org/CorpusID:18246616) ([Notebook](./domains/internal-dependencies/explore/ObjectOrientedDesignMetricsJava.ipynb)).
 - [Overview](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/overview-java/OverviewJava.md) contains overall statistics and details about methods and their complexity. ([Notebook](./jupyter/OverviewJava.ipynb)).
-- [Visibility Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/visibility-metrics-java/VisibilityMetricsJava.md) ([Notebook](./jupyter/VisibilityMetricsJava.ipynb)).
-- [Wordcloud](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/wordcloud/Wordcloud.md) contains a visual representation of package and class names ([Notebook](./jupyter/Wordcloud.ipynb)).
+- [Visibility Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/visibility-metrics-java/VisibilityMetricsJava.md) ([Notebook](./domains/internal-dependencies/explore/VisibilityMetricsJava.ipynb)).
+- [Wordcloud](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/wordcloud/Wordcloud.md) contains a visual representation of package and class names ([Notebook](./domains/internal-dependencies/explore/Wordcloud.ipynb)).
 - [Java Archetypes Treemap](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/anomaly-detection/JavaTreemap2ArchetypesOverviewPerDirectory.svg) ([Python Script](./domains/anomaly-detection/treemapVisualizations.py))
 
 ### :blue_book: Graph Data Science Reports

cypher/Metrics/Set_Incoming_Typescript_Module_Dependencies.cypher → cypher/Dependency_Enrichment/Set_Incoming_Typescript_Module_Dependencies.cypher

@@ -1,4 +1,4 @@
-// Set incoming Typscript Module dependencies
+// Set incoming Typescript Module dependencies
 
 // Get the top level dependency between a Typescript module and other modules that uses it
  MATCH (source:TS:Module)

cypher/Metrics/Set_Outgoing_Typescript_Module_Dependencies.cypher → cypher/Dependency_Enrichment/Set_Outgoing_Typescript_Module_Dependencies.cypher

@@ -1,4 +1,4 @@
-// Set outgoing Typscript Module dependencies
+// Set outgoing Typescript Module dependencies
 
 // Get the top level dependency between a Typescript module and an external modules it uses
  MATCH (source:TS:Module)